Biological Crystallography

 

Acta Cryst. (2003). D59, 1679-1687  [ doi:10.1107/S0907444903014987 ]

Structure of the heterodimeric neurotoxic complex viperotoxin F (RV-4/RV-7) from the venom of Vipera russelli formosensis at 1.9 Å resolution

M. Perbandt, I.-H. Tsai, A. Fuchs, S. Banumathi, K. R. Rajashankar, D. Georgieva, N. Kalkura, T. P. Singh, N. Genov and Ch. Betzel

Synopsis: The crystal structure of the presynaptic viperotoxin F from the venom of Vipera russelli formosensis at 1.9 Å resolution has been determined and compared with that of the neurotoxin vipoxin from the venom of Vipera ammodytes ammodytes.

PDB reference: 1oqs

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1688-1701  [ doi:10.1107/S0907444903015142 ]

Statistical density modification using local pattern matching

T. C. Terwilliger

Synopsis: Statistical density modification can make use of local patterns of density found in protein structures to improve crystallographic phases.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1702-1715  [ doi:10.1107/S0907444903015154 ]

Connectivity-based ab initio phasing: from low resolution to a secondary structure

N. Lunina, V. Lunin and A. Urzhumtsev

Synopsis: A connectivity-based phasing procedure starting from low resolution allows, in several favourable cases, identification of -helices and -strands in the corresponding ab initio phased Fourier maps.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1716-1724  [ doi:10.1107/S0907444903015403 ]

Three-beam interference is a sensitive measure of the efficacy of macromolecular refinement techniques

A. S. Soares, D. L. D. Caspar, E. Weckert, A. Héroux, K. Hölzer, K. Schroer, J. Zellner, D. Schneider, W. Nolan and R. M. Sweet

Synopsis: Triplet phases were recorded from rhombohedral insulin crystals and optimized for sensitivity to the correctness of the solvent model. The data were used to quantify the improvement of phases during model refinement, with emphasis on evaluating the solvent refinement strategy.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1725-1730  [ doi:10.1107/S0907444903015415 ]

Structure of apo, unactivated insulin-like growth factor-1 receptor kinase at 1.5 Å resolution

S. Munshi, D. L. Hall, M. Kornienko, P. L. Darke and L. C. Kuo

Synopsis: In order to obtain a high-resolution structure of apo, unactivated insulin-like growth factor-1 receptor kinase, a number of variants of IGFRK-0P were prepared and screened for crystallization. A double mutant with E1067A and E1069A substitutions within the kinase-insert region resulted in crystals that diffracted to 1.5 Å resolution. Overall, the structure of the mutant IGFRK-0P is similar to that of the wild-type IGFRK-0P structure with the exception of the previously disordered kinase-insert region in the wild type having become fixed.

PDB reference: 1p4o

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1731-1736  [ doi:10.1107/S0907444903015725 ]

MRSAD: using anomalous dispersion from S atoms collected at Cu K wavelength in molecular-replacement structure determination

J. P. Schuermann and J. J. Tanner

Synopsis: In-house sulfur-SAD phasing is demonstrated to be a useful method for overcoming model bias in molecular-replacement structure determination.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1737-1743  [ doi:10.1107/S0907444903015828 ]

Structure of the -amylase inhibitor tendamistat at 0.93 Å

V. König, L. Vértesy and T. R. Schneider

Synopsis: The atomic resolution crystal structure of tendamistat reveals a high degree of flexibility in the region that binds to pig pancreatic -amylase. This flexibility may contribute to the very tight binding between the inhibitor and the target enzyme.

PDB reference: 1ok0

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1744-1754  [ doi:10.1107/S0907444903016135 ]

Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 Å resolution

J. Koepke, E. I. Scharff, C. Lücke, H. Rüterjans and G. Fritzsch

Synopsis: The most reliable residues of squid-type DFPase were refined without restraints and in a subsequent full-matrix refinement cycle estimated standard deviations for bond lengths, bond angles, torsion angles, hydrogen bonds and calcium coordination distances could be obtained. These data were compared with the restraints applied in the preceding refinement cycles to compile a statistical analysis that constitutes a first step towards a set of restraints based solely on macromolecular data.

PDB reference: 1pjx

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1755-1761  [ doi:10.1107/S0907444903016068 ]

Effect of pH on the structure of rhizopuspepsin

B. V. L. S. Prasad and K. Suguna

Synopsis: An analysis of the crystal structure of rhizopuspepsin determined at various pH values shows structural changes leading to the unfolding of the enzyme at a high pH.

PDB references: 1uh7, 1uh9 and 1uh8

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1762-1766  [ doi:10.1107/S0907444903016214 ]

Unusual space-group pseudosymmetry in crystals of human phosphopantothenoylcysteine decarboxylase

N. Manoj and S. E. Ealick

Synopsis: Human phosphopantothenoylcysteine decarboxylase has been crystallized. The unit-cell parameters appear to be cubic and the Laue class appears to be m, but as a result of pseudosymmetry in the crystal the true space group has been identified as R3.

PDB reference: 1qzu

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1767-1772  [ doi:10.1107/S0907444903016287 ]

Using a quasi-parallel X-ray beam of ultrashort wavelength for high-pressure virus crystallography: implications for standard macromolecular crystallography

R. Fourme, É. Girard, R. Kahn, I. Ascone, M. Mezouar, A.-C. Dhaussy, T. Lin and J. E. Johnson

Synopsis: The first data acquisition from a virus crystal compressed at high pressure is reported. Results suggest that a quasi-parallel X-ray beam of ultrashort wavelength would improve conventional data collection.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1773-1781  [ doi:10.1107/S0907444903016652 ]

Structure of diferric hen serum transferrin at 2.8 Å resolution

P. Guha Thakurta, D. Choudhury, R. Dasgupta and J. K. Dattagupta

Synopsis: This study presents the three-dimensional structure of diferric hen serum transferrin (hST) at 2.8 Å resolution. The variations in interdomain and interlobe interactions, together with altered lobe orientations in hST with respect to other transferrins, particularly to its same gene product hen ovotransferrin, are discussed.

PDB reference: 1n04

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1782-1792  [ doi:10.1107/S0907444903016846 ]

Domain flexibility in the 1.75 Å resolution structure of Pb²⁺-calmodulin

M. A. Wilson and A. T. Brunger

Synopsis: An analysis of atomic mobility in the structure of Pb²⁺-loaded calmodulin indicates that the two structurally similar domains of the protein exhibit different types of flexibility. The structure also displays an intriguing form of disorder that results in a lattice consisting of alternating well ordered and poorly ordered domains.

PDB reference: 1n0y

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1793-1796  [ doi:10.1107/S0907444903016858 ]

A novel method of determining the number of macromolecules per asymmetric unit from accurate crystal-volume measurements

F. Li and T. A. Steitz

Synopsis: Using a new approach to make accurate measurements of the volume of a crystal, the authors developed a method to determine the number of macromolecules per asymmetric unit. This more accurate and convenient method has advantages over the traditional density-gradient methods.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1797-1800  [ doi:10.1107/S0907444903017414 ]

When less is more: a more efficient vapour-diffusion protocol

K. V. Dunlop and B. Hazes

Synopsis: A new method of reducing protein consumption by a modified vapour-diffusion protocol is described. In this protocol, the protein and mother liquor in the crystallization drop are both diluted, while the mother liquor in the well remains undiluted.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1801-1808  [ doi:10.1107/S090744490301936X ]

Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing

N. S. Pannu, A. J. McCoy and R. J. Read

Synopsis: The complex multivariate normal distribution provides the basis for a variety of methods in crystallography and leads to insights into the underlying assumptions in multiple isomorphous phasing.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1809-1812  [ doi:10.1107/S0907444903016123 ]

Expression, purification, crystallization and preliminary crystallographic analysis of the calponin-homology domain of Rng2

C.-H. Wang, M. Walsh, M. K. Balasubramanian and T. Dokland

Synopsis: The single calponin-homology domain of Rng2 from S. pombe has been overexpressed and purified. Monoclinic crystals have been obtained and Br- and Hg-derivative data sets have been measured to 2.21 Å using synchrotron radiation.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1813-1815  [ doi:10.1107/S0907444903016202 ]

Initial structural analysis of an ₄₄ C-type lectin from the venom of Crotalus durissus terrificus

M. T. Murakami, L. Watanabe, L. M. Gava, S. P. Zela, A. C. O. Cintra and R. K. Arni

Synopsis: A disulfide linked heterodimeric platelet-aggregation inducer has been crystallized and preliminary data have been obtained.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1816-1818  [ doi:10.1107/S0907444903015567 ]

Crystallization of the PX domain of cytokine-independent survival kinase (CISK): improvement of crystal quality for X-ray diffraction with sodium malonate

Y. Xing and W. Xu

Synopsis: The Phox homology domain of cytokine-independent survival kinase and its phosphoinositide complex have been crystallized using sodium malonate as the precipitant and cryoprotectant. The native protein crystal diffracted to 1.6 Å.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1819-1821  [ doi:10.1107/S090744490301607X ]

Cloning, purification, crystallization and preliminary crystallographic analysis of galactokinase from Pyrococcus furiosus

D. de Geus, A. P. Hartley, S. E. Sedelnikova, S. E. Glynn, P. J. Baker, C. H. Verhees, J. van der Oost and D. W. Rice

Synopsis: Galactokinase from P. furiosus has been crystallized and a MAD data set has been collected to 2.9 Å.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1822-1823  [ doi:10.1107/S090744490301610X ]

Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus

J. Akerboom, A. P. Turnbull, D. Hargreaves, M. Fisher, D. de Geus, S. E. Sedelnikova, J. M. Berrisford, P. J. Baker, C. H. Verhees, J. van der Oost and D. W. Rice

Synopsis: Phosphoglucose isomerase from P. furiosus has been crystallized and MAD data have been collected to 1.92 Å resolution.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1824-1827  [ doi:10.1107/S0907444903016056 ]

Crystallization and initial X-ray diffraction studies of higher plant photosystem I

A. Ben-Shem, N. Nelson and F. Frolow

Synopsis: Complete higher plant photosystem I (PSI) complex containing the PSI reaction centre and the light-harvesting complex LHCI has been crystallized and characterized; diffraction data were collected to 4.44 Å resolution.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1828-1830  [ doi:10.1107/S090744490301641X ]

Crystallization, data collection and phasing of black-eyed pea trypsin/chymotrypsin inhibitor in complex with bovine -trypsin

J. A. R. G. Barbosa, R. C. L. Teles, V. P. Forrer, B. G. Guimarães, F. J. Medrano, M. M. Ventura and S. M. Freitas

Synopsis: Crystals of the complex between black-eyed pea trypsin and chymotrypsin inhibitor (BTCI) and bovine -trypsin diffracted to 2.36 Å resolution and belong to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a = 59.3, b = 61.8, c = 80.0 Å.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1831-1833  [ doi:10.1107/S0907444903016445 ]

Crystallization and preliminary X-ray analysis of the atrial natriuretic peptide (ANP) receptor extracellular domain complex with ANP: use of ammonium sulfate as the cryosalt

H. Ogawa, X. Zhang, Y. Qiu, C. M. Ogata and K. S. Misono

Synopsis: The extracellular hormone-binding domain of the atrial natriuretic peptide receptor (rat) has been expressed, purified, and crystallized in hormone-bound form from 2.0 M ammonium sulfate. X-ray data were collected to 3.1 Å with the crystals frozen in 3.4 M ammonium sulfate used as the cryoprotectant.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1834-1837  [ doi:10.1107/S0907444903016573 ]

Crystallization of the GMPPCP complex of the NG domains of Thermus aquaticus Ffh and FtsY

I. V. Shepotinovskaya, P. J. Focia and D. M. Freymann

Synopsis: Crystallization of a nucleotide-dependent complex of the NG domains of the SRP GTPases Ffh and FtsY is reported.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1838-1839  [ doi:10.1107/S0907444903017128 ]

Crystallization and preliminary X-ray crystallographic study on a xyloglucan-specific exo--glycosidase, oligoxyloglucan reducing-end specific cellobiohydrolase

K. Yaoi, H. Kondo, M. Suzuki, N. Noro, S. Tsuda and Y. Mitsuishi

Synopsis: OXG-RCBH from Geotrichum sp. M128 hydrolyzes the reducing end of oligoxyloglucan and produces two glucosyl residue segments. Crystals of the enzyme have been obtained and X-ray data have been collected to a resolution of 2.2 Å.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1840-1842  [ doi:10.1107/S090744490301713X ]

Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8

S. Yoshiba, N. Nakagawa, R. Masui, T. Shibata, Y. Inoue, S. Yokoyama and S. Kuramitsu

Synopsis: An ADP-ribose pyrophosphatase from an extreme thermophile, T. thermophilus HB8, has been crystallized. X-ray diffraction data were collected to 1.50 Å resolution.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1843-1845  [ doi:10.1107/S0907444903017712 ]

Crystallization and preliminary X-ray diffraction studies of nucleoside diphosphate kinase from Thermus thermophilus HB8

S. Takeishi, N. Nakagawa, N. Maoka, M. Kihara, M. Moriguchi, R. Masui and S. Kuramitsu

Synopsis: Nucleoside diphosphate kinase from T. thermophilus HB8 was overexpressed in Escherichia coli, purified and crystallized. A complete native data set to 1.9 Å resolution has been collected.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1846-1848  [ doi:10.1107/S0907444903017864 ]

Crystallization and preliminary X-ray diffraction studies of Aes acetyl-esterase from Escherichia coli

N. Sorrentino, G. De Simone, V. Menchise, L. Mandrich, M. Rossi, G. Manco and C. Pedone

Synopsis: The acetyl-esterase Aes from E. coli has been crystallized. The crystals belong to space group P2₁2₁2₁ and diffract to 2.5 Å resolution.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1849-1852  [ doi:10.1107/S0907444903018006 ]

Expression, purification, crystallization and preliminary X-ray diffraction studies of recombinant class B non-specific acid phosphatase of Salmonella typhimurium

R. D. Makde, V. Kumar, G. D. Gupta, J. Jasti, T. P. Singh and S. K. Mahajan

Synopsis: The aphA gene from a pathogenic strain of S. enterica sv. Typhimurium, which encodes a class B non-specific acid phosphatase, has been cloned in the multicopy plasmid pBluescript SK^-. Recombinant AphA purified from E. coli DH5 crystallizes in space group P2₁2₁2₁, with a = 112.4, b = 130.2, c = 139.6 Å.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1853-1855  [ doi:10.1107/S090744490301802X ]

Crystallization and preliminary crystallographic analysis of RSB-66, a novel round spermatid-specific protein

M. Yang, S. Li, G. Liang, L. Sun, X. Zhang, N. Liu, H. Pang, S. Miao, L. Wang and Z. Rao

Synopsis: The crystallization and preliminary X-ray data of a novel round spermatid specific protein:RSB-66 are presented.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1856-1858  [ doi:10.1107/S0907444903018146 ]

Expression, crystallization and preliminary crystallographic analysis of the extracellular IgV-like domain of the human natural killer cell inhibitory receptor p75/AIRM1

N. Dimasi, L. Moretta, R. Biassoni and R. A. Mariuzza

Synopsis: p75/AIRM1, also known as Siglec-7, is a sialoadhesin expressed on natural killer cells that inhibits their cytolytic activity. It is composed of an extracellular region comprising one IgV-like and two IgC-like domains. The extracellular IgV-like domain, believed to be involved in target-cell recognition, has been expressed in E. coli, folded in vitro and crystallized.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1859-1862  [ doi:10.1107/S0907444903018067 ]

Preliminary structure analysis of the DH/PH domains of leukemia-associated RhoGEF

R. Kristelly, B. T. Earnest, L. Krishnamoorthy and J. J. G. Tesmer

Synopsis: Crystals of the DH/PH domains of leukemia-associated RhoGEF (LARG) have been produced and diffract to 2.05 Å spacing using a synchrotron X-ray source. Xenon and NaBr derivatives were generated and the isomorphous and anomalous Patterson maps were analyzed.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1863-1865  [ doi:10.1107/S0907444903018250 ]

Protein preparation, crystallization and preliminary X-ray crystallographic studies of a thermostable hypoxanthine-guanine phosphoribosyltransferase from Thermoanaerobacter tengcongensis

D. You, Q. Chen, Y. Liang, J. An, R. Li, X. Gu, M. Luo and X.-D. Su

Synopsis: Native and His-tagged mutant (L160I) T. tengcongensis hypoxanthine-guanine phosphoribosyltransferase with bound IMP and GMP have been crystallized in space groups C222₁ and I222, respectively. X-ray diffraction data were collected to 2.2 and 1.7 Å, respectively.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1866-1868  [ doi:10.1107/S0907444903018328 ]

Crystallization and preliminary crystallographic analysis of the importin--SREBP-2 complex

S. J. Lee, T. Sekimoto, E. Yamashita, E. Nagoshi, A. Nakagawa, H. Tanaka, Y. Yoneda and T. Tsukihara

Synopsis: The complex of importin- and the HLHZ domain of SREBP-2 has been crystallized in the orthorhombic space groups P2₁2₁2₁ and C222₁.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1869-1870  [ doi:10.1107/S0907444903018389 ]

Purification, crystallization and preliminary X-ray analysis of the novel DEAD protein BstDEAD from Bacillus stearothermophilus

A. B. Carmel and B. W. Matthews

Synopsis: DEAD proteins are members of a large and diverse family of RNA helicases. The cloning, expression, purification and crystallization of a putative member of this family from B. stearothermophilus that has a unique extension outside of the core region is described.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1871-1873  [ doi:10.1107/S0907444903018468 ]

Purification and crystallization of Escherichia coli pseudouridine synthase RluD

M. Del Campo, J. Ofengand and A. Malhotra

Synopsis: RluD, a 23S ribosomal RNA multi-site specific pseudouridine synthase from E. coli, has been crystallized. MAD data were collected to 2.0 Å on an SeMet derivative and structure determination is in progress.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1874-1876  [ doi:10.1107/S0907444903016883 ]

Polystyrene microbridges used in sitting-drop crystallization release 1,4-diphenyl-2-butene, a novel inhibitor of human MAO B

F. Hubálek, C. Binda, M. Li, A. Mattevi and D. E. Edmondson

Synopsis: 1,4-Diphenyl-2-butene, a competitive MAO B inhibitor that interferes with the binding of MAO B inhibitors, was found to originate from polystyrene microbridges used for MAO B crystallization.

Online 19 September 2003

 

Acta Cryst. (2003). D59, 1877-1880  [ doi:10.1107/S0907444903016871 ]

High-phasing-power lanthanide derivatives: taking advantage of ytterbium and lutetium for optimized anomalous diffraction experiments using synchrotron radiation

É. Girard, P. L. Anelli, J. Vicat and R. Kahn

Synopsis: Two neutral lanthanide complexes, Yb-HPDO3A and Lu-HPDO3A, are shown to be excellent compounds to obtain high-phasing-power heavy-atom derivatives. SAD experiments with hen egg-white lysozyme derivative crystals indicate that these compounds are particularly interesting for optimized anomalous diffraction experiments using synchrotron radiation.

Online 19 September 2003